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Freiburg RNA Tools

• ... all about RNA

MoDPepInt Server

• Domain Interaction

CPSP-Tools Server

• HP Lattice Proteins

Galaxy-FR

• RNA tool workflows
  and infrastructure

Teaching

RNA structure

• counting
  number of structures
• Nussinov
  structure with max. #bp
• McCaskill
  structure probabilities
• MEA
  max. exp. accuracy

RNA-RNA interaction

• co-folding
  linked prediction
• hybrid-only
  max. intermol. bps
• accessibility
  of interacting sites

Sequence alignment

• Needleman-Wunsch
  global, linear gap cost
• Hirschberg
  global, linear gap cost
• Waterman-Smith-Beyer
  global, arbitrary gap cost
• Gotoh
  global, affine gap cost
• Smith-Waterman
  local, linear gap cost
• Gotoh (Local)
  local, affine gap cost
• Arslan-Egecioglu-Pevzner
  local, length-normalized
• Feng-Doolittle
  multiple, progressive
• Iterative Refinement
  multiple, progressive
• Notredame-Higgins-Heringa
  multiple, t-coffee

Evol. Clustering

• Agglomerative Clustering
  Evol. tree generation